PfizerFragmenter
- pydantic model openff.qcsubmit.workflow_components.PfizerFragmenter[source]
The openff.fragmenter implementation of the Pfizer fragmenation method as described here (doi: 10.1021/acs.jcim.9b00373)
Show JSON schema
{ "title": "PfizerFragmenter", "description": "The openff.fragmenter implementation of the Pfizer fragmenation method as described here\n(doi: 10.1021/acs.jcim.9b00373)", "type": "object", "properties": { "type": { "title": "Type", "default": "PfizerFragmenter", "enum": [ "PfizerFragmenter" ], "type": "string" }, "target_torsion_smarts": { "title": "Target Torsion Smarts", "description": "The list of SMARTS patterns used to identify central target bonds to fragment around. By default this is any single non-termial bond.", "type": "array", "items": { "type": "string" } } } }
- Config
allow_mutation: bool = True
validate_assignment: bool = True
- Fields
target_torsion_smarts (Optional[List[str]])
type (Literal['PfizerFragmenter'])
- Validators
check_environments
»target_torsion_smarts
- classmethod description()[source]
Returns a friendly description of the workflow component.
- Return type
- apply(molecules, toolkit_registry, processors=None, verbose=True)
This is the main feature of the workflow component which should accept a molecule, perform the component action and then return any resulting molecules.
- Parameters
molecules (List[openff.toolkit.topology.molecule.Molecule]) – The list of molecules to be processed by this component.
toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) – The openff.toolkit.utils.ToolkitRegistry which declares the available backend toolkits to be used.
processors (Optional[int]) – The number of processor the component can use to run the job in parallel across molecules, None will default to all cores.
verbose (bool) – If true a progress bar should be shown on screen.
- Returns
A component result class which handles collecting together molecules that pass and fail the component
- Return type
- classmethod fail_reason()
Returns a friendly description of why a molecule would fail to pass the component.
- Return type
- provenance(toolkit_registry)
Collect the toolkit information and add the fragmenter version information.
- Parameters
toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) –
- Return type
- field target_torsion_smarts: Optional[List[str]] = None
The list of SMARTS patterns used to identify central target bonds to fragment around. By default this is any single non-termial bond.
- Validated by
check_environments